Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNAnull mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that several lncRNAs are differentially expressed both in time and space, with some presenting highly restricted expression in only selected brain regions. We further demonstrate altered regulation of genes for a large variety of cellular pathways and processes upon deletion of the lncRNA loci. Finally, we found that 4 of the 13 lncRNAs significantly affect the expression of several neighboring proteincoding genes in a cis-like manner. By providing insight into the endogenous expression patterns and the transcriptional perturbations caused by deletion of the lncRNA locus in the developing and postnatal mammalian brain, these data provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease.T he exquisite complexity of the mammalian brain derives from its vast diversity of neuronal and glial cell types (1, 2). The specification and differentiation of such a variety of cell types during brain development is finely orchestrated spatiotemporally by the regulation of complex transcriptional programs. Increasing evidence points to a role for long noncoding RNAs (lncRNAs) as key regulatory elements of this process. Intriguingly, within the mammalian body, the largest repertoire and diversity of lncRNA genes outside the germ line occurs in the brain (3-10), where lncRNAs exhibit regional and cell-specific localization (6, 10). Although many unanswered questions remain regarding the functional activity and molecular mechanisms of lncRNA loci, the expression patterns of lncRNAs may serve as a proxy signal for important, context-specific biological activity.A role for lncRNA genes in brain development and function is supported by the fact that ablation of two lncRNA loci, Evf2 and Pantr2 (linc-Brn1b), perturbs neuronal development (11, 12). Loss of Evf2, a developmentally regulated lncRNA that controls transcriptional activity through cooperation with the homeodomain protein DLX-2 (11), leads to abnormal development and synaptic function of hippocampal GABAergic interneurons (11). Similarly, ablation of the Pantr2 locus results in a decreased number of intermediate progenitors in the developing telencephalon, reduced neurons in L2/3 of the cerebral cortex, and disorganization of the barrel cortex (12). Furthermore, human genetic studies have pointed to lncRNAs as potential factors in brain disorders (10,(13)(14)(15)(16).To gain preliminary insights into the functional and physiological relevance of lncRNA loci in vivo, we previously generated knockout (KO) mouse models of ...